/*
 * MX Cheminformatics Tools for Java
 *
 * Copyright (c) 2007-2009 Metamolecular, LLC
 *
 * http://metamolecular.com
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 *
 * Copyright (C) 2009-2010  Syed Asad Rahman <asad@ebi.ac.uk>
 *
 * Contact: cdk-devel@lists.sourceforge.net
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
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 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
 */

using NCDK.SMSD.Algorithms.Matchers;
using System;
using System.Collections.Generic;

namespace NCDK.SMSD.Rings
{
    // @cdk.module smsd
    // @author Syed Asad Rahman <asad@ebi.ac.uk> 2009-2010
    [Obsolete("This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK and a newer, more recent version of SMSD is available at http://github.com/asad/smsd .")]
    public class RingFilter
    {
        private IRingFinder ringFinder;
        private static readonly IComparer<IList<IAtom>> comparator = new RingSizeComparator();
        private IAtomMatcher filter;
        private IAtomContainer mol;

        public RingFilter(IAtomMatcher filter, IRingFinder finder)
        {
            ringFinder = finder;
            this.filter = filter;
        }

        public void FilterAtoms(int atomLimit, ICollection<IList<IAtom>> rings, ICollection<IAtom> atoms)
        {
            foreach (var ring in rings)
            {
                if (atoms.Count >= atomLimit)
                {
                    break;
                }

                if (RingMatches(ring))
                {
                    foreach (var atom in ring)
                        atoms.Add(atom);
                }
            }
        }

        public void FilterAtoms(IAtomContainer molecule, ICollection<IAtom> atoms)
        {
            this.mol = molecule;
            var rings = new List<IList<IAtom>>(ringFinder.FindRings(molecule));
            rings.Sort(comparator);

            foreach (var ring in rings)
            {
                if (atoms.Count == molecule.Atoms.Count)
                {
                    break;
                }

                if (RingMatches(ring))
                {
                    foreach (var atom in ring)
                        atoms.Add(atom);
                }
            }
        }

        private bool RingMatches(IList<IAtom> ring)
        {
            foreach (var atom in ring)
            {
                if (!filter.Matches(mol, atom))
                {
                    return false;
                }
            }

            return true;
        }

        private class RingSizeComparator : IComparer<IList<IAtom>>
        {
            public int Compare(IList<IAtom> o1, IList<IAtom> o2)
            {
                if (o1.Count > o2.Count) return +1;
                if (o1.Count < o2.Count) return -1;
                return 0;
            }
        }
    }
}
